The genetic determinants of coreceptor usage reside in the HIV envelope, in particular, the V3 loop. Consequently, this region is highly useful for the training and development of computerized genotypic predictors of coreceptor usage, which have the potential to make the screening and testing of HIV-infected patients (1).
Determination of HIV-1 tropism by bioinformatics-based genotypic rules, such as support vector machines (SVMs) is now available.

For HIV-1 subtype B, the bioinformatic algorithms based using HIV V3 genotype data were able to achieve high concordance with the phenotypic assays, approaching the degree of agreement between phenotype assays themselves (2-4). The specificity of tropism genotypic assays is high to detect X4 or R5X4 viruses. This can be done on HIV RNA, as well as on HIV DNA (5, 10).
A false positive rate adjusted at 10% with geno2pheno provides the best balance between specificity and sensitivity for predicting the X4 or R5X4 tropism (6-9).
Geno2Pheno (FPR: 10%) has been validated for HIV-1 subtype B and subtype C (11).
Geno2Pheno (FPR: 5%) has been validated for HIV-1 subtype CRF02-AG and subtype D (13, 14).

For HIV-1 subtype CRF01-AE the following algorithm has been validated.

HIV-1 subtype

Genotypic rule for tropism prediction1

Subtype CRF01-AE (12)

(i) R or K at position 11 and/or K at position 25 of V3
(ii) R at position 25 of V3 and a net charge of ≥+5
(iii) a net charge of ≥+6
(iv) loss of the N-linked glycosylation site2 in V3 and a net charge of ≥+4

1 One of the following criteria is required for predicting CXCR4 coreceptor usage
2 The glycosylation site is NXT with X for any amino acid; the site is lost if the NXT motif is mutated
Note: The V3 net charge is calculated by subtracting the number of negatively charged amino acids [D and E] from the number of positively charge ones [K and R]

For other non-B subtypes, we recommend to use a phenotypic method for determining the virus tropism.
References